Pre! sites have been released for three new species: Atlantic cod (Gadus morhua), Nile tilapia (Oreochromis niloticus) and domestic ferret (Mustela putorius furo).

The Atlantic cod annotation will be released on our main site for Ensembl release 65, while Nile tilapia and domestic ferret will be available in later releases.

The Atlantic cod assembly gadMor1, provided by the cod genome consortium, has undergone a full gene annotation. The final gene set, displayed here, comprises 20,095 protein-coding genes, 518 pseudogenes, and 1,541 noncoding RNA genes. Click here to go to the Atlantic cod pre site.

The Nile tilapia assembly Orenil1.0, provided by the Broad Institute, has undergone preliminary annotation. This Pre! site displays 20248 raw gene models predicted from alignments of vertebrate proteins in UniProt. Alignments of zebrafish and stickleback Ensembl proteins from release 62 are also available, as are ab initio gene predictions and alignment of sequences from several public databases (e.g. UniGene, EMBL Vertebrate RNA, UniProt). RNASeq data are expected for the Nile tilapia and we intend to make use of these data during the forthcoming analyses. Click here to go to the Nile tilapia pre site.

The domestic ferret assembly MusPutFur1.0 was also provided by the Broad Institute. This Pre! site includes alignments of ferret proteins, cDNAs and ESTs. In addition, ab initio gene predictions and alignment of sequences from several public databases (e.g. UniGene, EMBL Vertebrate RNA, UniProt) are available. Click here to go to the domestic ferret pre site.

All gene annotations in Ensembl are supported by biological sequence alignments. These sequences used as supporting evidence are downloaded from public databases, for example UniProt and ENA, at the start of the gene annotation process. Public sequence databases are updated regularly, meaning that sequences are added to and removed from them. We don’t update our gene sets every release; for some species the gene annotations may not be updated for several releases. It follows that gene annotations in the Ensembl gene sets may be supported by biological sequences that have been withdrawn from the public databases.

In order to indicate these changes, we now flag sequences that we have used as supporting evidence but which have been withdrawn from the public databases. These flags are updated every release by checking all protein-coding transcripts and exons for all species against the most current sequence databases. Transcripts based on evidence that has been withdrawn are flagged and coloured grey (instead of yellow) on the Transcript’s Supporting Evidence page. Transcripts supported by only a grey protein sequence should be considered less well supported. Below is the example of the transcript ENSGGOT00000034302 from the gorilla which was built using the human protein A6NKB4.2

In addition to sequences from external public databases, Ensembl translations from well-annotated species may also be used as supporting evidence for annotation in other species, particularly primates and species with fragmented assemblies. Withdrawn Ensembl translations are flagged in the same way as described above.

You can also access these data programmatically using the API by looking for the transcript attribute “NoEvidence”.

Single Species private MySQL

Ensembl has just made it even easier to access genome data in the cloud. We are pleased to announce the availability of pre-configured Ensembl MySQL EC2 cloud images. These are pre-built images that allow you to run your own private single species MySQL instances on EC2, the full list is here. There are images for each of our species; just start one up and connect with the API (or mysql client) just as you would with ensembldb, or useastdb – except this MySQL server you’ll have for exclusive use. You’ll also have full root permissions on the instance so you can configure, tweak and restart the MySQL server as you wish.

Getting started

Experienced users of Amazon EC2 need only to skip to the full list of AMIs on the ensembl website and when launching to ensure security group access to port 5306 on your instance.

If you’re not already familiar with Amazon EC2 and would like to get started with ensembl in the cloud then the following set of brief instructions should be enough get you going. The steps are:

1. Set up your Amazon EC2 Account
2. Instantiate the Ensembl Image
3. Connect to the instance

Signing up for your amazon EC2 account is simple if you don’t already have one. Just go to http://aws.amazon.com/ec2 and click Sign Up for Amazon EC2. Then follow the on screen instructions.

Launching an instance is just as simple when you use the amazon EC2 launch wizard. The amazon AWS documentation describes the process expertly, and can be found here. To launch the Ensembl Amazon Machine Image(AMI) follow the  documentation beginning at Step 1 to launch the wizard. We shall digress at step 2, “choosing an AMI” where instead select an Ensembl AMI from the list here. As an example, we select Homo sapiens with id  ami-b0fb5

Ensure that you are in the useast region (which is the default) and in the launcher wizard select the community AMI tab (the green arrow in the figure below) and paste in ami-dccb0fb5 to the box incated with the red arrow and underlined in red.

After clicking Select, for best performance choose the Large(m1.large, 7.5GB) instance type from the dropdown, although you may also choose the smaller Micro(t1.micro) type which would incur a lower cost per hour http://aws.amazon.com/ec2/#pricing

Click Continue and follow on with steps 3 & 4 from the amazon docs to create a key-pair. Next create a security group (firewall rule) that will allow access to our MySQL instance. The process is described in detail as step 5 of the amazon docs, with the exception that we require only ports 22 for ssh access and port 5306 to allow access to the MySQL server (don’t forget to click Apply Rule Changes).

Take particular note on the point of caution from the docs regarding restricting access to specific IP addresses.

The quick-start security group enables all IP addresses to access your instance over the specified ports (e.g., SSH). This is acceptable for the short exercise in this tutorial, but it’s unsafe for production environments. In production, you’ll authorize only a specific IP address or range of addresses to access your instance

Finally launch the instance as described in step 6 and record the public DNSname of your new server.

If all has been successful you will now have a private AWS instance running a MySQL server with a single Ensembl species, which is Homo sapiens in the case of this exercise.

Connecting to the instance

To connect to the instance you do so as:

mysql <PUBLIC_DNS_NAME> -u anonymous -P5306

If you cannot connect, check that the instance is running and also review that the security group settings are correct, both ports 22 and 5306 need to be open.

You may ssh directly to the instance with the username ‘ensembl’ as described here.

ssh -i <YOUR_KEYPAIR> ensembl@<PUBLIC_DNS_NAME>

The Ensembl MySQL AMI comes pre-installed and configured with the current perl API and you can run your scripts against Ensembl from within this instance, but targeting MySQL on localhost:5306 rather than the public DNS name.

Amazon bill by the hour so don’t forget to terminate the instance when you have finished.

Full details of  Amazon AWS costs and charges are here http://aws.amazon.com/ec2/#pricing and be aware that you are billed for both storage, and EC2 time, it is your responsibility to monitor your usage.

We have reviewed our archive retention policy, and it has been decided that we will now retain archive versions of the main Ensembl website for three years, rather than two as previously advertised. Archives will now be automatically retired on a rolling schedule, as and when they become more than three years old, except as stated below.

Please note that all databases are archived indefinitely and can still be accessed on our public server using the corresponding version of the API, and all versions of our code can still be checked out of CVS; only the web interfaces maintained by the Sanger Institute have a limited lifespan, owing to hardware constraints.

In addition to the past three years’ archives, we will retain a limited number of older sites in order to support the previous assembly of our key model species (human, mouse and zebrafish).

The following archives are scheduled for retirement at the end of June 2011:

• 35 (Nov 2005)
• 38 (Apr 2006)
• 43 (Feb 2007)
• 47 (Oct 2007)
• 48 (Dec 2007)
• 49 (Mar 2008)

Release 46 (Aug 2007) will be retained for the forseeable future as it is the last release containing mouse assembly NCBI m36.

To find out which archive supports a particular assembly, please see the assembly table on the main Ensembl website.

We’re always looking at ways we can improve the Ensembl browser experience.  Quite often this results in a focus on the speed at which a particular display or track can be provided.  Over the past year or so we have been generating various pre-computed data which is compressed and optimised for web display purposes.  For release 62 we took the step of moving some of this data outside of the database into binary files.

The signal plot or ‘wiggle’ style displays provided as part of the regulation evidence (see ‘Functional genomics’ in the config panel) are now served from collection or ‘col’ files.  This provides significant speed ups, allowing many more tracks to be turned on without adversely affecting the response time of the display.  In fact it is now possible to turn on all the current signal plots for human, that’s 334 distinct data sets!

Moving the data outside of the database also overcomes various constraints and issues with managing the data and much reduces the size of the funcgen database.  This is beneficial for those who want to download the funcgen databases for API access only, for those running mirror sites if you want to display the signal plots you will need to down load the col files.

We intend to broaden support for standard data formats (e.g. BAM etc) as we identify more data which is amenable to flat file access.  As these data are not contained in the MySQL data dumps, we have created a new area on the FTP site:

    ftp.ensembl.org/pub/current_data_files

More information can be found in the README files contained in this directory.

We’d like to announce our beta site at beta.ensembl.org.  This site will allow us to show you the latest features of our website, and to get user feedback before new functionality and design are moved over to our live site.

Come by and try it out!  Leave us feedback by clicking on the black Feedback button at the right of beta pages.

Our latest features on the beta site are listed on the front page.  Two of the ones we’re most excited about are:

1) Track ordering on region in detail.  Want to change the order of data tracks on the genome?  Either use the bar at the left, or reorder them using Configure this page.  You can even move them all to one side of the chromosome (at the moment, Ensembl separates them by strand.)  See our help page for more.

2) Draw features for selected species in alignment views in the location tab.  For example, add a species to multi-species view.  Click on configure this page at the left.  A species menu is now shown, so you can draw data tracks for one species and not the other, if you like!  See the bottom of the help page for more about this functionality.

As many of you will know, Ensembl now provides three website mirrors, in addition to the main site (http://www.ensembl.org/) located near Cambridge in the UK. These are:

• US West http://uswest.ensembl.org/
• US East http://useast.ensembl.org/
• Asia http://asia.ensembl.org/

Until the beginning of March we were only automatically redirecting users in the US, Canada and Japan to US West; the other mirrors were only reachable by explicitly visiting the appropriate mirror URL.

By “automatically redirecting” we mean looking at the IP address of each visitor, figuring out roughly where they were located, and sending them to the nearest mirror, a process referred to as Geo-IP-based redirection.

Since the beginning of March, we’ve been increasing the amount of redirection we do. Now, users in the eastern US are redirected to http://useast.ensembl.org/ and users in Australasia are redirected to http://asia.ensembl.org/. You may see a message to this effect the first time the redirect happens. You can of course override the redirection if you want to.

Users in the western US and Japan continue to be redirected to US West; we will be doing some tests over the next few weeks to see if Japanese users will get better performance from the US West or Asia mirrors.

For those interested, we’re using the free version of MaxMind’s GeoLite City which gives us the level of granularity we need, and has proven to be very reliable.

As always, please let us know your experiences of using the mirrors via the Helpdesk.

Happy holidays from Ensembl! Here in Hinxton, we are planning new developments for the new year (what else would we do with all this snow!) Some of the highlights planned for early next year include:

• The first gene set for turkey in Ensembl, and inclusion of turkey into pairwise (between two species) whole-genome alignments and multiple species alignments (including a new 3-way avian alignment).

• Inclusion (merge) of manual curation of the zebra-fish genome by the HAVANA group into the Ensembl gene set.

• Update to dbSNP 132 for variations in the human genome.

• Sea Urchin (Strongylocentrotus purpuratus) and Honey Bee (Apis mellifera) genomes in the Ensembl Metazoa site. See other upcoming species to Ensembl genomes here.

Don’t forget, an overview of upcoming annotation to Ensembl is on our roadmap.

For those of you going on holiday soon, enjoy! We look forward to supporting all your cutting-edge scientific endeavors in 2011.

The Ensembl Team